#!/bin/bash

#SBATCH -J IQTree-cat_15cephala_nozorro_compopass                          # Job name 
#SBATCH -o IQTree-cat_15cephala_nozorro_compopass.%A.out                    # File to which stdout will be written
#SBATCH -e IQTree-cat_15cephala_nozorro_compopass.%A.err                    # File to which stderr will be written
#SBATCH --mail-type=ALL                         # BEGIN,END,ALL
#SBATCH --mail-user=vknutson@g.harvard.edu   # Email address
#SBATCH -n 1                                    # Number of tasks
#SBATCH -c 64                                   # Number of threads/processors/cpus per task
#SBATCH --contiguous
#SBATCH -t 06-00:00                             # Runtime in DD-HH:MM
#SBATCH --mem 512000                            # Memory for all cores in Mbytes (--mem-per-cpu for MPI jobs)
#SBATCH -p bigmem                               # Partition shared, serial_requeue, unrestricted, interact

module purge
module load gcc/7.1.0-fasrc01 openmpi/2.1.0-fasrc02 iqtree/1.5.5-fasrc02

#individual run specifying actual input file

srun -n $SLURM_NTASKS -c $SLURM_CPUS_PER_TASK --mpi=pmi2 --export=ALL iqtree-omp-mpi -nt $SLURM_CPUS_PER_TASK \
-st AA -ninit 10 -bb 1500  -msub nuclear -s 15cephala_compopass.phy \
-m MFP+MERGE -rcluster 10 -madd LG4M,LG4X,LG+C10,LG+C20,LG+C30,LG+C40,LG+C50,LG+C60 -mrate G,R,E

# -b standard non parametric bootstrap (500); -bb ultrafastbootstrap (minimum 1000)
# CAT-like models are mainly used for non-partition analysis, to avoid over parametrization
# -o for outgroup name e.g. -o $3


